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Series GSE56622 Query DataSets for GSE56622
Status Public on Jul 28, 2014
Title Ribosome profiling upon glucose starvation in S. cerevisiae
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions.
Overall design Examination of mRNA translation in S. cerevisiae upon glucose starvation.
Contributor(s) Zid BM, O'Shea EK
Citation(s) 25119046
Submission date Apr 08, 2014
Last update date May 15, 2019
Contact name Brian Matthew Zid
Organization name University of California San Diego
Department Chemistry and Biochemistry
Lab Zid
Street address 9500 Gilman Drive
City La Jolla
State/province California
ZIP/Postal code 92093
Country USA
Platforms (2)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (22)
GSM1365918 BY-Ribo_logphase_Replicate1
GSM1365919 EY-Ribo_logphase_Replicate1
GSM1365920 BY-RNA_logphase_Total_Replicate1
BioProject PRJNA244101
SRA SRP041039

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GSE56622_ZidProcessedDataAll.txt.gz 1.4 Mb (ftp)(http) TXT
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